ModView

ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments.

As a Netscape plugin,like Chime, it can be embed into Web pages and controlled by Javascript objects on the page. It has wide range of
tools to manipulate and analyze sequences and
structures by interactive control

Some ModView Highlights

ModView works with hundreds protein structures and/or sequences.
Can easily be interface with either local or internet structure and/or sequence databases.
Provides integrative vidual analyses of PSI-BLAST profile and phylogenetic data
Provides visualization and fast manipulation of multiple sequence-alignment based 3-D structures
Allows manually and automatically editing, coloring and viewing of multiple sequence alignments.

... ModView as Front-end interface to biodatabases and servers

Modview can easily interface with local or remote bioresources to provide GUI and analytical tools. Currently ModView is used as a database interface in several structure-sequence protein resources.

ModBase, a Database of Comparative Protein Structure Models, (Pieper et. al, Nuc.Acid.Res.)

LigBase, a Structural Database of Aligned Ligand Binding Protein Sequences, (Stuart et al., Bioinformatics).

DBAli, a Database of Sequence-Structure alignments, (Marti-Renom et. al.2001,Bioinformatics).

ModView can be also used to view structures and sequences in Protein Data Bank . Choose 'Rasmol' display option on the 'View Structure' page at PDB.

InterPreTS, an Interaction Prediction through Tertiary Structure server at EMBL, (Aloy, P & Russell, RB (2002) Proc Natl Acad Sci USA. 99, 5896-5901.Aloy, P & Russell, RB (2002) Bioinformatics. Submitted. )
Protein Network (de Brevern A.G., Etchebest. C. and Hazout S. (2000), Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks, Proteins: Structures, Functions and Genetics, 41(3), 271-287).

... ModView provides Protein Family analysis.

Two families of DNA binding proteins have been analysed by ModView. The scalable multiple alignment with combination of visualization of structural features of molecules cleary shows invariant residues involved in DNA binding in Zinc finger protein superfamily (ZFP) and superfamily of the DNA-Binding Domain Of The Replication Initiation Protein E1 From Papillomavirus (RIP). These two families also shows different pictures of homology tree. ZFP family has ~50% identity among all the members, while RIP family can be subdivided in several closely related subfamilies. (Ilyin and Sali, 2001, CSHL).

Recently, ModView facilitates the target selection process for New York Structural Genomics Research Consortium, by providing integrative visual analyses of the comparative protein models, PSI-BLAST profile and phylogenetic data of protein targets selected for novel structures determination (Bonanno et. al. 2001, PNAS).

... ModView References.

* V.A.Ilyin, U. Pieper, A. C. Stuart, M. A. Mart-Renom and A. Sali. Analysis and Visualization of Multiple Biomolecule Structures and Sequences by ModView. (submitted)

* Ursula Pieper, Narayanan Eswar, Ashley C. Stuart, Valentin A. Ilyin and Andrej Sali, MODBASE, a database of annotated comparative protein structure models. Nucleic Acids Research. 2002. Jan 1: 30(1):255-9. PubMed

* Stuart A.C., Ilyin V.A., and Sali A., (2001) LigBase: A Database of Families of Aligned Ligand Binding Sites in Known Protein Sequences and Structures, Bioinformatics 2002 Jan;18(1):200-1 PubMed

* Jeffrey B. Bonanno, Carme Edo, Narayanan Eswar, Urusla Pieper, Valentin Ilyin, Michael J. Romanowski, Sue Ellen Gerhaman, Helen Kycia, F. William Sudier, Andrej Sali, Stephen Burley. Structural genomics of enzymes involved in sterol/isoprenoid biosynthesis. Proc Natl Acad Sci U S A 2001 Nov 6;98(23):12896-901. PubMed

* Valentin Ilyin and Andrej Sali. Protein superfamily analysis by ModView. CSHL meeting. Aug.8, 2001.

* Marti-Renom, M.A., Ilyin V.A., Sali, A. DBAli: A database of protein structure alignments. Bioinformatics. p.746. Vol. 17 no 8, 2001. PubMed

Modview uses Roger Sayle's Rasmol rendering system and modified alignment editor panel from Michele Clamp's Jalview.

Old ModView link at the Andrej Sali lab

email to Valentin Ilyin:

http://mozart.bio.neu.edu/
414 Mugar, Biology
Northeastern University
360 Huntigton Ave, Boston, MA 02115
tel. (617) 373-7032 • fax (617)-373-3724